What has changed since you made the backup ? assuming backup was 100% a ok. Software certainly has changed - assuming you let your Fedora did or did yourself, usual updates.
Is the hardware the same?
Smells to me a bit like "power" issues - two usb ports - is it how power is supplied to the drive, exclusively this way? Perhaps usb does not supply enough of it - I'd try a different source, maybe external to the computer psu.
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